ClinVar Miner

Variants studied for digestive tract malformation

Included ClinVar conditions (84):
Minimum submission review status: Collection method:
Minimum conflict level:
Gene type:
ClinVar version:

If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign risk factor not provided total
837 240 2058 833 375 2 2 4226

Gene and significance breakdown #

Total genes and gene combinations: 120
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign risk factor not provided total
RECQL4 60 17 840 247 64 0 0 1227
KMT2D 160 135 212 128 34 0 2 616
ZEB2 89 9 128 69 28 0 0 307
FRAS1 15 2 181 65 44 0 0 301
FREM2 6 1 163 33 29 0 0 231
GLI3 43 1 85 80 38 0 0 230
MED12 7 4 72 36 25 0 0 144
TTC7A 25 1 58 13 15 0 0 109
SALL1 23 0 35 37 18 0 0 106
DYNC2H1 83 14 5 0 0 0 0 98
TBX3 7 0 40 36 16 0 0 97
GRIP1 2 0 50 8 7 0 0 66
FOXC1 23 6 14 4 6 0 0 52
AAAS 12 3 28 6 1 0 0 48
PITX2 19 3 11 9 3 0 0 44
KDM6A 15 13 9 1 1 0 0 39
TBX1 5 0 23 1 9 0 0 37
WDR60 9 1 7 3 12 0 0 32
FANCB 0 0 11 13 6 0 0 30
WDR35 10 5 7 5 4 0 0 30
SALL4 18 0 3 1 4 0 0 26
SOX2, SOX2-OT 20 0 4 1 0 0 0 25
MID1 17 5 2 0 0 0 0 24
WDR34 13 0 2 3 6 0 0 24
FLNA 3 0 13 0 0 0 0 16
PTEN 4 1 11 0 0 0 0 16
PQBP1 8 0 3 3 1 0 0 15
ZIC3 2 0 5 9 0 0 0 15
RFX6 9 2 1 0 0 0 0 12
MNX1 11 0 0 0 0 0 0 11
MYCN 9 1 0 0 1 0 0 11
CENPF 7 2 1 0 0 0 0 10
MCFD2, TTC7A 0 0 5 2 1 0 0 8
ASIC4, GMPPA 5 0 2 0 0 0 0 7
BRCA2 5 0 2 0 0 0 0 7
AIFM3, ARVCF, C22orf39, CDC45, CLDN5, CLTCL1, COMT, CRKL, DGCR2, DGCR6L, DGCR8, ESS2, FAM230A, GGTLC3, GNB1L, GP1BB, GSC2, HIRA, KLHL22, LZTR1, MED15, MRPL40, P2RX6, PI4KA, PRODH, RANBP1, RIMBP3, RTL10, RTN4R, SCARF2, SEPTIN5, SERPIND1, SLC25A1, SLC7A4, SNAP29, TANGO2, TBX1, THAP7, TMEM191B, TRMT2A, TSSK2, TXNRD2, UFD1, USP41, ZDHHC8, ZNF74 5 1 0 0 0 0 0 6
KIFBP 1 0 3 0 2 0 0 6
LOC111721705, ZEB2 4 0 2 0 0 0 0 6
PHOX2B 2 0 2 0 0 2 0 6
UBR1 6 0 0 0 0 0 0 6
CCNQ 5 0 0 0 0 0 0 5
HCCS 4 1 0 0 0 0 0 5
CLMP 4 0 0 0 0 0 0 4
COX7B 3 0 1 0 0 0 0 4
DDN, KMT2D 0 0 1 3 0 0 0 4
FREM1 3 0 1 0 0 0 0 4
PALB2 2 0 2 0 0 0 0 4
SOX2 4 0 0 0 0 0 0 4
​intergenic 3 0 0 0 0 0 0 3
HSPA9 3 0 0 0 0 0 0 3
KLLN, PTEN 0 0 3 0 0 0 0 3
MYCN, MYCNOS 3 0 0 0 0 0 0 3
NDUFB11 2 0 1 0 0 0 0 3
SPECC1L, SPECC1L-ADORA2A 2 1 0 0 0 0 0 3
AIFM3, ARVCF, C22orf39, CDC45, CLDN5, CLTCL1, COMT, CRKL, DGCR2, DGCR6, DGCR6L, DGCR8, ESS2, FAM230A, GGT2, GGTLC3, GNB1L, GP1BB, GSC2, HIC2, HIRA, KLHL22, LZTR1, MED15, MRPL40, P2RX6, PI4KA, PRODH, RANBP1, RIMBP3, RIMBP3B, RTL10, RTN4R, SCARF2, SEPTIN5, SERPIND1, SLC25A1, SLC7A4, SNAP29, TANGO2, TBX1, THAP7, TMEM191B, TRMT2A, TSSK2, TXNRD2, UFD1, USP18, USP41, ZDHHC8, ZNF74 2 0 0 0 0 0 0 2
AIFM3, ARVCF, C22orf39, CDC45, CLDN5, CLTCL1, COMT, CRKL, DGCR2, DGCR6L, DGCR8, ESS2, FAM230A, GGT2, GGTLC3, GNB1L, GP1BB, GSC2, HIC2, HIRA, KLHL22, LZTR1, MED15, MRPL40, P2RX6, PI4KA, PRODH, RANBP1, RIMBP3, RIMBP3B, RTL10, RTN4R, SCARF2, SEPTIN5, SERPIND1, SLC25A1, SLC7A4, SNAP29, TANGO2, TBX1, THAP7, TMEM191B, TRMT2A, TSSK2, TXNRD2, UFD1, USP41, ZDHHC8, ZNF74 2 0 0 0 0 0 0 2
C22orf39, CDC45, CLDN5, CLTCL1, DGCR2, ESS2, GP1BB, GSC2, HIRA, MRPL40, PRODH, SEPTIN5, SLC25A1, TBX1, TSSK2, UFD1 2 0 0 0 0 0 0 2
CLMP, LOC112042785 2 0 0 0 0 0 0 2
DACT1 1 0 0 1 0 0 0 2
KMT2A 2 0 0 0 0 0 0 2
LOC110120888, TBX1 2 0 0 0 0 0 0 2
NEK1 2 0 0 0 0 0 0 2
AAAS, C12orf10 1 0 0 0 0 0 0 1
AATF, ACACA, C17orf78, DDX52, DHRS11, DUSP14, GGNBP2, HNF1B, LHX1, MRM1, MYO19, PIGW, SYNRG, TADA2A, ZNHIT3 1 0 0 0 0 0 0 1
ABCC5, ABCF3, ACTL6A, ALG3, AP2M1, ATP11B, B3GNT5, C3orf70, CAMK2N2, CCDC39, CHRD, CLCN2, DCUN1D1, DNAJC19, DVL3, ECE2, EEF1AKMT4, EEF1AKMT4-ECE2, EHHADH, EIF2B5, EIF4G1, EPHB3, FAM131A, FXR1, GNB4, HTR3C, HTR3D, HTR3E, IGF2BP2, KCNMB2, KCNMB3, KLHL24, KLHL6, LAMP3, LINC00888, LINC01014, LINC01206, LINC01839, LINC01840, LINC01994, LINC01995, LINC02015, LINC02031, LINC02053, LINC02054, LINC02069, LIPH, LOC101928739, LOC101928882, LOC102724604, LOC107986163, LOC108281177, LOC110120606, LOC110120632, LOC110120734, LOC110121064, LOC112935913, LOC114004376, MAGEF1, MAP3K13, MAP6D1, MCCC1, MCF2L2, MFN1, MIR1224, MIR4448, MIR5588, MRPL47, NDUFB5, PARL, PEX5L, PIK3CA, POLR2H, PSMD2, SENP2, SNORA63D, SNORA63E, SNORD66, SOX2, SOX2-OT, SOX2-SRR2, THPO, TMEM41A, TTC14, USP13, VPS8, VWA5B2, YEATS2, ZMAT3, ZNF639 0 1 0 0 0 0 0 1
ABR, BHLHA9, TRARG1, YWHAE 0 0 0 1 0 0 0 1
ADA2, ATP6V1E1, BCL2L13, BID, CECR2, CECR3, GAB4, HDHD5, IL17RA, MICAL3, PEX26, SLC25A18, TMEM121B, TUBA8, USP18 1 0 0 0 0 0 0 1
ADA2, CECR3, GAB4, HDHD5, IL17RA, TMEM121B, XKR3 1 0 0 0 0 0 0 1
ADARB1, C21orf58, COL18A1, COL6A1, COL6A2, DIP2A, FAM207A, FTCD, LINC00163, LINC00315, LINC00334, LSS, MCM3AP, PCBP3, PCNT, POFUT2, PRMT2, S100B, SLC19A1, SPATC1L, YBEY 1 0 0 0 0 0 0 1
AGMO 0 0 0 1 0 0 0 1
AIFM3, ARVCF, C22orf39, CDC45, CLDN5, CLTCL1, COMT, CRKL, DGCR2, DGCR6, DGCR6L, DGCR8, ESS2, FAM230A, GGTLC3, GNB1L, GP1BB, GSC2, HIRA, KLHL22, LZTR1, MED15, MRPL40, P2RX6, PI4KA, PRODH, RANBP1, RIMBP3, RTL10, RTN4R, SCARF2, SEPTIN5, SERPIND1, SLC25A1, SLC7A4, SNAP29, TANGO2, TBX1, THAP7, TMEM191B, TRMT2A, TSSK2, TXNRD2, UFD1, USP41, ZDHHC8, ZNF74 1 0 0 0 0 0 0 1
ALPK3, NMB, PDE8A, SEC11A, SLC28A1, WDR73, ZNF592, ZSCAN2 0 0 0 1 0 0 0 1
ANKS1B, UHRF1BP1L 0 0 0 1 0 0 0 1
AOPEP, FANCC 1 0 0 0 0 0 0 1
ARVCF, C22orf39, CDC45, CLDN5, CLTCL1, COMT, DGCR2, DGCR6L, DGCR8, ESS2, GNB1L, GP1BB, GSC2, HIRA, MRPL40, PRODH, RANBP1, RTL10, RTN4R, SEPTIN5, SLC25A1, TANGO2, TBX1, TRMT2A, TSSK2, TXNRD2, UFD1, ZDHHC8 1 0 0 0 0 0 0 1
ARVCF, COMT, GNB1L, GP1BB, LOC110120888, LOC112694764, LOC112694766, MIR4761, RTL10, SEPT5-GP1BB, SEPTIN5, TBX1, TXNRD2 1 0 0 0 0 0 0 1
AXIN1 1 0 0 0 0 0 0 1
B3GNTL1, METRNL, TBCD 0 0 0 1 0 0 0 1
BBS10 1 0 0 0 0 0 0 1
BRIP1 1 0 0 0 0 0 0 1
C12orf60, GUCY2C 1 0 0 0 0 0 0 1
CCDC74A, MZT2A, TUBA3D 0 0 0 1 0 0 0 1
CDH13 0 1 0 0 0 0 0 1
CHST5 0 0 0 1 0 0 0 1
CHST7, DIPK2B, DUSP21, EFHC2, FUNDC1, KDM6A, KRBOX4, MAOA, MAOB, MIR221, MIR222, NDP, RP2, SLC9A7, ZNF674 0 1 0 0 0 0 0 1
CNTNAP2 0 0 0 1 0 0 0 1
CTNNB1 0 1 0 0 0 0 0 1
DIPK2B, DUSP21, EFHC2, FUNDC1, KDM6A, MAOA, MAOB, NDP 0 1 0 0 0 0 0 1
DNAJC15, EPSTI1 0 0 0 1 0 0 0 1
DNMT3B 0 0 1 0 0 0 0 1
ENPEP, PITX2 1 0 0 0 0 0 0 1
FAM170A 0 1 0 0 0 0 0 1
FAM98C 0 1 0 0 0 0 0 1
FBP1, FBP2 0 0 0 1 0 0 0 1
FLNA, LOC107988032 0 0 1 0 0 0 0 1
FOXC1, FOXF2, FOXQ1, GMDS 1 0 0 0 0 0 0 1
FOXF1 0 1 0 0 0 0 0 1
FXYD4, HNRNPF 0 1 0 0 0 0 0 1
GLI3, LOC110121152 0 0 1 0 0 0 0 1
GMPPA 1 0 0 0 0 0 0 1
GPC5 0 0 0 1 0 0 0 1
GTDC1, LINC01412, LOC105373656, LOC110120671, LOC110121209, LOC111721705, LOC112806051, TEX41, ZEB2 1 0 0 0 0 0 0 1
HCFC1 0 0 1 0 0 0 0 1
HOXD13 0 0 1 0 0 0 0 1
INTU 1 0 0 0 0 0 0 1
KMT2B 0 0 1 0 0 0 0 1
MIR17HG 1 0 0 0 0 0 0 1
NALCN 0 0 0 1 0 0 0 1
NREP 0 0 0 1 0 0 0 1
PARM1 0 0 0 1 0 0 0 1
PRDM5 0 0 1 0 0 0 0 1
PTCH1 0 1 0 0 0 0 0 1
SIX6 0 0 1 0 0 0 0 1
SMYD3 0 0 0 1 0 0 0 1
SORCS1 0 0 0 1 0 0 0 1
SOX2, SOX2-OT, SOX2-SRR2 1 0 0 0 0 0 0 1
SPTAN1, WDR34 1 0 0 0 0 0 0 1
TCTEX1D2 1 0 0 0 0 0 0 1
TMEM256, TMEM256-PLSCR3 0 1 0 0 0 0 0 1
ZBTB24 0 0 1 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 79
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign risk factor not provided total
Invitae 215 45 1157 372 229 0 0 2018
Illumina Clinical Services Laboratory,Illumina 1 1 708 427 144 0 0 1279
OMIM 266 0 2 0 0 2 0 270
Center for Human Genetics, Inc 24 103 42 26 1 0 0 196
Genetic Services Laboratory, University of Chicago 72 9 42 1 0 0 0 124
Fulgent Genetics,Fulgent Genetics 20 1 95 0 0 0 0 116
Dan Cohn Lab,University Of California Los Angeles 71 2 2 0 0 0 0 75
GeneReviews 48 0 0 0 1 0 0 49
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 0 3 40 0 0 43
Molecular Genetics Laboratory,Children's Mercy Hospital and Clinics 31 0 0 0 0 0 0 31
Molecular Pathology, SA Pathology 20 1 5 0 0 0 0 26
Baylor Genetics 17 1 5 0 0 0 0 23
Reutter Lab, Institute of Human Genetics,University Hospital Bonn 2 5 0 15 0 0 0 22
Baylor-Hopkins Center for Mendelian Genomics,Johns Hopkins University 7 6 7 0 0 0 0 20
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 20 0 0 0 0 20
Shaikh Laboratory, University of Colorado 0 16 0 0 0 0 0 16
Genomic Research Center,Shahid Beheshti University of Medical Sciences 4 2 9 0 0 0 0 15
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 0 0 1 13 0 0 14
GeneDx 8 0 1 0 0 0 0 9
Laboratoire de Cytogenetique,Hospices Civils de Lyon 4 2 3 0 0 0 0 9
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 0 1 1 6 0 0 8
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children 6 1 0 0 0 0 0 7
Molecular Genetics Laboratory,BC Children's and BC Women's Hospitals 6 1 0 0 0 0 0 7
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 4 3 0 0 0 0 0 7
Center of Genomic medicine, Geneva,University Hospital of Geneva 5 2 0 0 0 0 0 7
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne 2 5 0 0 0 0 0 7
Victorian Clinical Genetics Services,Murdoch Childrens Research Institute 4 2 0 0 0 0 0 6
Institute of Human Genetics,University of Goettingen 2 2 1 0 0 0 0 5
Shenzhen Institute of Pediatrics,Shenzhen Children's Hospital 2 1 1 1 0 0 0 5
UCLA Clinical Genomics Center, UCLA 1 4 0 0 0 0 0 5
University of Washington Center for Mendelian Genomics,University of Washington 0 5 0 0 0 0 0 5
International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine 5 0 0 0 0 0 0 5
Bioscientia Institut fuer Medizinische Diagnostik GmbH,Sonic Healthcare 4 0 1 0 0 0 0 5
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 4 0 0 0 0 4
Institute of Human Genetics,Klinikum rechts der Isar 3 1 0 0 0 0 0 4
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 2 2 0 0 0 0 0 4
Foundation for Research in Genetics and Endocrinology,Institute of Human Genetics 2 2 0 0 0 0 0 4
Paul Sabatier University EA-4555, Paul Sabatier University 0 1 0 3 0 0 0 4
Centre de Biologie Pathologie Génétique,Centre Hospitalier Universitaire de Lille 2 2 0 0 0 0 0 4
SIB Swiss Institute of Bioinformatics 1 3 0 0 0 0 0 4
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 2 0 2 0 0 0 0 4
Molecular Diagnostics Laboratory,M Health: University of Minnesota 1 3 0 0 0 0 0 4
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 2 1 0 0 0 0 0 3
Institute of Human Genetics,Cologne University 3 0 0 0 0 0 0 3
Mendelics 3 0 0 0 0 0 0 3
Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine 1 0 2 0 0 0 0 3
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 2 1 0 0 0 0 3
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement,Assistance Publique Hopitaux de Paris 3 0 0 0 0 0 0 3
Laboratory of Medical Genetics,National & Kapodistrian University of Athens 3 0 0 0 0 0 0 3
Institute of Human Genetics,Friedrich-Alexander-Universität Erlangen-Nürnberg 1 0 1 0 0 0 0 2
Centre for Genomic and Experimental Medicine,University of Edinburgh 2 0 0 0 0 0 0 2
Clinical Genetics, Erasmus University Medical Center 2 0 0 0 0 0 0 2
Talkowski Laboratory, Center for Human Genetic Research,Massachusetts General Hospital 2 0 0 0 0 0 0 2
Center for Human Genetics and Laboratory Diagnostics, Dr. Klein, Dr. Rost and Colleagues 1 1 0 0 0 0 0 2
Centre for Mendelian Genomics,University Medical Centre Ljubljana 1 1 0 0 0 0 0 2
Institute of Experimental Endocrinology,Slovak Academy of Sciences 1 1 0 0 0 0 0 2
GenomeConnect, ClinGen 0 0 0 0 0 0 2 2
SBielas Lab, Department of Human Genetics,University of Michigan 1 0 1 0 0 0 0 2
Clinical Genetics Group,University of Otago 2 0 0 0 0 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 1 0 0 0 0 0 0 1
Molecular Genetics Laboratory,London Health Sciences Centre 0 0 0 1 0 0 0 1
ARUP Laboratories, Cytogenetics and Genomic Microarray,ARUP Laboratories 1 0 0 0 0 0 0 1
Department of Medical Genetics,Oslo University Hospital 0 1 0 0 0 0 0 1
Laboratory of Molecular Oncology,N.N. Petrov Institute of Oncology 0 0 1 0 0 0 0 1
Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia,Universidade Católica de Brasília 1 0 0 0 0 0 0 1
Laboratory of Human Genetics,Universidade de São Paulo 1 0 0 0 0 0 0 1
Ludwig Lab, Institute of Human Genetics, University Hospital Bonn 0 1 0 0 0 0 0 1
Center of Medical Genetics and Primary Health Care 1 0 0 0 0 0 0 1
Ege University Pediatric Genetics,Ege University 1 0 0 0 0 0 0 1
Genetic and Metabolic Disease Program, Children's Medical Center Research Institute,UT Southwestern Medical Center at Dallas 0 1 0 0 0 0 0 1
Biocant - Biotechnology Innovation Center 1 0 0 0 0 0 0 1
Pediatrie Multidisciplinaire,Assitance Publique des Hopitaux de Marseille 1 0 0 0 0 0 0 1
The Raphael Recanati Genetics Institute,Rabin Medical Center 1 0 0 0 0 0 0 1
Division of Critical Care, Department of Pediatrics,Cardinal Glennon Children's Hospital 1 0 0 0 0 0 0 1
Johns Hopkins Genomics,Johns Hopkins University 1 0 0 0 0 0 0 1
Children’s Hospital, Clinical research laboratory,Medizinische Fakultaet Carl Gustav Carus, Technische Universitaet Dresden 1 0 0 0 0 0 0 1
Medical Genetics,Necip Fazıl Sehir Hastanesi 1 0 0 0 0 0 0 1
Biochemistry Laboratory of CDMU,Chengde Medical University 1 0 0 0 0 0 0 1
Klinisk genetik och genomik Research,Gothenburg University 1 0 0 0 0 0 0 1

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